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• NPK affects flowering time and intensity, and fruiting in cacao. • Low NPK delays flowering and reduces its intensity. • Excess N reduces flowering compared with optimal N. • Fruiting numbers increase with increasing N dose. • Pollen viability and germination are not affected by NPK availability. Cacao (Theobroma cacao L.) is a globally significant perennial crop primarily cultivated in tropical regions, where it provides employment to millions of people. Crop productivity is chronically low, and it is imperative to have good information on the cacao plant nutrient demands to maximize yield. The objective of this study was to assess the effects of nitrogen (N), phosphorus (P), and potassium (K) availability on flowering time, flowering intensity, pollen viability, and fruiting of cacao (Theobroma cacao L.). An F1 segregating population of the CCN-51 cultivar was studied, as this is a well-defined commercially important hybrid cultivar, and because the vast majority of cacao is grown from hybrid seeds. Using a lysimeter setup, young seedlings were grown from the age of 9 months with different levels of N, P, and K loads. Low N, P, and K doses significantly delayed flowering time and reduced the number of flower cushions and flowering intensity. At the highest N dose, flowering intensity was lower than at intermediate N doses. Pollen viability and germination, on the other hand, were not affected by changes in N, P, and K input concentrations. Flowering intensity was the same on the trunk and canopy of a given tree, regardless of the treatment. Nitrogen availability played an important role in natural fruit set in this first year of fruiting, with increasing N resulting in increasing natural fruit set. This study shows the importance of N, P and K optimization for cacao reproduction. Optimizing nutrient availability could have a great impact on its productivity and yield. [ABSTRACT FROM AUTHOR]

• Cacao orchards exhibited alternation between high and low productive seasons. • Individual trees showed regular, irregular or alternate seasonal fruiting patterns. • Marked alternate pattern of pod production only concerned 19 % of trees. • Seasonal flowering was regular in crown and more variable on trunk. • Exogenous factors synchronized seasonal flowering and fruiting among trees. Theobroma cacao , a tropical cauliflorous fruit tree, typically produces flowers and fruits twice a year and exhibits alternate harvesting patterns over consecutive six-monthly seasons in regions with bi-modal rainfall distribution, such as Côte d'Ivoire. This study investigated seasonal variations in flowering and fruiting among trees in populations of mixed cacao genotypes. The intensities of crown and trunk flowering and pod production were monitored for eight consecutive six-monthly seasons on 114 adult cacao trees grown from seedlings. We investigated distributions of seasonal flowering and fruiting values, relationships between flowering and pod production, and the effects of seasonal cumulative rainfall. The patterns of seasonal flowering and fruiting series were analyzed using two descriptors: the first distinguishing between regular and variable patterns, and the second analyzing the structure of such variability, classifying it as either irregular or alternating. Despite being subjected to similar climate and agronomic management, individual trees exhibited highly variable flowering and fruiting behaviors within each season, as well as variable patterns of flowering and fruiting across seasons. Seasonal alternate fruiting on a population scale masked highly variable patterns among trees, and only 19 % of the trees exhibited marked alternate fruiting patterns. Variations in pod production on a tree scale were mainly related to variations in trunk flowering. Endogenous factors seemed to control seasonal variations in flowering and fruiting, even though exogenous factors, both climatic and agronomic, could structure flowering and fruiting patterns at the orchard scale. [Display omitted] [ABSTRACT FROM AUTHOR]

• Water deficit reduced leaf water potential in cocoa leaves by a factor three. • Leaf water potential was higher in the hybrid Mercedes (M) than in the clone (CI03) in non-irrigated trees, suggesting greater access to soil water for M. • Drought-induced reductions in leaf and crown size lowered leaf surface area and sap flux density. • Leaf and crown responses to irrigation were strongly genotype-specific, suggesting substantial genotypic differences in drought tolerance. Cocoa trees are highly sensitive to water stress but these negative effects may differ genetically and may be mitigated by potassium (K) application. We studied these effects on six-year-old adult trees, five genotypes produced by somatic-embryogenesis, and one by cross pollination (Hybrid), grown under sub-optimal field conditions in central Côte d'Ivoire. Trees were subjected to two soil water treatments (with or without dry season irrigation) and two K fertilization levels (with and without K). We assessed interactive effects of treatments on several leaf and crown traits: sap flux density (SF), leaf water potential (LWP), stomatal conductance (Gs), leaf size (LS), specific leaf area (SLA), leaf water content (LWC), leaf area index (LAI), light interception, litterfall and a visual index of whole-plant water stress (WSI). Mixed-effects model results revealed that withholding irrigation negatively affected SF, LWP, Gs, LS, SLA, LAI and light capture and increased WSI scores. Potassium application did not significantly mitigate the negative effects of withholding irrigation. A significant effect of genotype was observed for most of the monitored leaf physiological, morphological and crown traits. Furthermore, we found significant, positive interactions between genotype and irrigation for SF, LWP, leaf area, LS, SLA, LWC, LAI and intercepted light, suggesting that the differences in observed responses to drought conditions are genotype-specific. These results provide insights into the acclimation strategies of cocoa and genetic variation therein, and can be used to select drought-tolerant genotypes. [ABSTRACT FROM AUTHOR]

• We studied the effect of pruning on the branching of young cocoa trees. • Pruning a section of a branch increased branching toward the tip of the branch. • Pruning entire branches increased branching along the entire length of the retained branches. • These new insights help design pruning strategies and develop a 3D cocoa model. The branching pattern of a tree determines the efficiency of light interception and carbon assimilation. Pruning can modify the branching pattern, because of changes in physiological and environmental conditions, and ultimately pruning can have major effects on yield. For one of the major tropical tree crops, cocoa (Theobroma cacao), very little is known about branching response to pruning. To address this knowledge gap, we performed a pruning experiment on young cocoa trees in Côte d'Ivoire. We applied five treatments to two parcels planted with different genetic materials: two heading treatments (the removal of the terminal apex or 66% of a primary branch) and two thinning treatments (the removal of 1 or 2 primary branches) and one unpruned control. The secondary-branching pattern of the primary branches was described by the number, position, and length of secondary branches right after pruning, and the same observations were repeated after a cycle of leaf production. The probability of branching and the length of secondary branches along a primary branch, in pruned and unpruned conditions, was analyzed using generalized and linear mixed effect models, respectively. In unpruned conditions, the probability of secondary-branch presence was higher towards the middle of the primary branches and lower at the base and the tip. Secondary-branch length decreased from the base to the tip of a primary branch. After one cycle of leaf production, secondary branch emergence differed between the two parcels. In one parcel more branches emerged on the distal section of a primary branch, while in the other they emerged preferentially in the more proximal section. Pruning increased the probability of branch emergence mostly towards the tip of a primary branch, with heavy heading having the strongest effect. By contrast, heavy thinning increased branch emergence also toward the base of the primary branch. Our results can be applied to improve formation pruning, as this may trigger branching in different parts of the crown, depending on the form of pruning. Our study also assists the development of three-dimensional tree models that could further our understanding of the impact of pruning on cocoa growth and productivity. [ABSTRACT FROM AUTHOR]

• Doses of Pb and Pb+Fe did not interfere with the predawn leaf water potential (ΨWL) of plants. • There was a differential accumulation of Pb and Fe in the roots and leaves. • Most of Fe and Pb uptake by the root system predominantly accumulated in the roots and only a small fraction was translocated to the shoot. • Leaf enzymatic antioxidant metabolism was altered, mainly by flooding, in relation to Pb and Pb+Fe doses applied in soil. • Flooding and doses of Pb affected proteins related to photosynthesis, DNA, antioxidative system and carbohydrate metabolism. Under natural conditions, plants can be affected by several types of abiotic stresses, such as flooding and the accumulation of toxic metals in the soil. Pb is a non-essential metallic element for plants and is highly toxic for living beings. Fe, as an essential micronutrient, is involved in fundamental plant processes, such as photosynthesis. The main objective of this work was to evaluate the proteomic profiles and the activity of key enzymes of leaf antioxidant metabolism in juvenile plants of the CCN 51 cacao genotype, grown in flooding soil and subjected to a dose of Pb and to different equimolar doses of Pb+Fe. Doses of Pb and Pb+Fe did not interfere with the predawn leaf water potential (Ψ WL) of plants, but soil flooding was a key factor for the decline of Ψ WL. There was a differential accumulation of Pb and Fe in the roots and leaves, both in flooded soil and non-flooded. Most of Fe and Pb uptake by the root system predominantly accumulated in the roots and only a small fraction was translocated to the shoot, regardless of the water content in the soil. Flooding and the variation of Pb+Fe doses in the soil did not change the transport of Pb to the plant shoot since there were no major alterations in the levels of Pb in the leaves. Leaf enzymatic antioxidant metabolism was altered, mainly by flooding, in relation to Pb or Pb+Fe doses applied in soil. The time of exposure of plants to stressor factors was important for the changes in the activity of key enzymes of the leaf antioxidant metabolism. Soil flooding, with doses of 2 mmol Pb kg−1 soil + 0.5 mmol Fe kg−1 soil, at 6 and 24 h after treatment application, had a greater influence on Ψ WL , antioxidant enzymatic metabolism and leaf proteome, and affected proteins related to photosynthesis, DNA, antioxidative system and carbohydrate metabolism, whose abundance was overexpressed or repressed compared to the control. [ABSTRACT FROM AUTHOR]

• g s is regulated fundamentally by Ψ leaf , and kept until Ψ leaf reaching values of −1.7 MPa. • Two rootstocks are identified as potential tolerant to water deficit candidates. • Three rootstock-scion combinations are identified as potential tolerant to water deficit. • Rootstock drought tolerance is not influenced by a greater contact surface of the root with the soil. Adverse effects caused by drought on cacao seedlings can produce significant yield losses and require a better understanding of plant-tolerance mechanisms in order to overcome them. The selection of drought-tolerant rootstocks is a key strategy to achieve greater resilience in water-limited environments. This study aimed to assess leaf ecophysiological responses and growth of four rootstocks and 24 rookstock-scion combinations to water deficit. Leaf stomatal conductance (g s), leaf water potential (Ψ leaf) and relative quantum yield of PSII (Φ PSII) were measured in irrigated and non-irrigated seedlings. Data were recorded 14 and 20 days after irrigation was suspended in the non-irrigated seedlings. Biomass of leaf, stem and root as well root volume were determined 24 days after irrigation was withheld. The EET-400 rootstock showed significantly higher values of Ψ leaf at both 14 and 20 days under water deficit. This rootstock and IMC-67 showed the highest g s after 14 days without irrigation The relationship between Ψ leaf and g s showed that the combinations of rootstock EET-400 with scions EET-575, EET-576 and EETP-800 exhibited the highest values of g s and Ψ leaf. The lower root volumes found under the water deficit condition in EET-400 and IMC-67 demonstrate that tolerance to water deficit by cacao rootstocks is not influenced by a greater contact surface of the root with the soil. [ABSTRACT FROM AUTHOR]

• Cocoa is an important crop for millions of small holders, but low farm-level yields mean sustainable intensification is required urgently. • Modelling the response of cocoa yield to variation in rainfall would allow the response of cocoa to management to be estimated. • A time lag model (using a delayed differential equation) to simulate the effect of rainfall on cocoa seasonality was developed. • Parameterised using real cocoa yield data, the model outputs gave a good likeness to the observed on-farm yield response. • These results indicate high potential to develop this model to incorporate other climatic variables and farm management practices. Cocoa (Theobroma cacao) is an economically important crop grown by approximately six million of smallholder farmers throughout the tropics and sub-tropics. However, farm level yields are often very low, and sustainable intensification is urgently required. Assessing the impact of on-farm interventions of farm productivity and profitability requires an understanding of the contribution of inter-annual climate variability to cocoa yields. A Delayed Differential Equation model (DDE) was used to simulate the effect of rainfall on cocoa yields. A DDE model is an ordinary differential equation model that incorporates time lags, and is therefore able to incorporate the delay in yield response to rainfall due interactions with the cocoa flowering and the pod development processes. The DDE was constructed and based on regional rainfall and farm-level cocoa yield data from 96 farms across the main cocoa growing regions in Ghana. Model outputs indicate that a good likeness of seasonality in crop production was achieved. The potential to conduct a detailed parameterisation and extend this model to include other parameters such as agrochemical inputs and farm management practices are discussed. By further developing this model into a useful tool to predict and understand variability in cocoa yield, the sustainable intensification of small holder cocoa farming is supported. [ABSTRACT FROM AUTHOR]

Abstract Black pod caused by Phytophthora species is a devastating disease of cacao (Theobroma cacao L.) in production regions worldwide. Breeding for cacao genotypes resistant to black pod disease is crucial for sustainable cocoa production and profitability. Although breeding programmes in the past have made considerable efforts in improving resistance of cocoa genotypes with diverse genetic background, the disease continues to cause unacceptable yield losses in cacao production. To understand the mode of inheritance of epicuticular wax on the surface of cocoa pod known to play a major role in resistance to black pod disease, a 6 × 6 full diallel and a M x N (6 × 4) mating designs were used and data was analysed using Griffing's method I model I approach and the North Carolina design –II approach, respectively. The results of the two mating designs were consistent and showed that epicuticular wax on leaf and pod surfaces of cacao were under the control of additive genetic effects. The non-additive effects were generally much smaller compared to the additive genetic effects. The significant association between GCA estimates of parents and their means indicates that parental values could be used as indicators of progeny performance. The best general combiners for epicuticular wax load on leaf and pod surfaces were Pa7/808, T60/887 and Pa 150. The larger additive components and heritability observed in this study, indicates that pedigree selection could be used to develop cacao cultivars with high amount of epicuticular wax on pod surface to enhance resistance to black pod disease. [ABSTRACT FROM AUTHOR]

Somatic embryogenesis (SE) has been routinely used as mass micropropagation technique, and as a model system for investigating the structural, physiological, and molecular events occurring during somatic embryo development. Successful in vitro SE is related to the quality and yield of somatic embryos obtained. In cacao ( Theobroma cacao L.) SE, the efficiency of somatic embryo production has improved with secondary SE. However, the low number of somatic embryos able to conversion into viable plantlets is still low. Then, two morphological types of normal mature somatic embryos can be identified during cacao secondary SE. The first type shows white appearance and high conversion potential (75%), while the second type shows translucent appearance and exhibit low conversion potential (15%). In order to investigate the proteins that can be associated to conversion potential in cacao somatic embryos, the mass spectrometry HDMS E proteomic approach was used. At least 60 proteins showed differences in abundance levels in cacao white somatic embryos, when compared to translucent. An increased abundance of Beta-glucosidase, NAD(P)-linked oxidoreductase and Electron transfer flavoprotein proteins were observed in white somatic embryos. Moreover, in translucent somatic embryos were observed an increased abundance of Cytochrome P450 and Pathogenesis-related proteins. Using white somatic embryos as a model, we suggest that carbohydrate metabolism process and the redox regulation are involved in the control/regulation of somatic embryo quality. These new findings may improve cacao SE protocol, as well as the understanding of the role of pivotal metabolic pathways associated to this in vitro morphogenetic route. [ABSTRACT FROM AUTHOR]

Regression models to predict leaf area and leaf weight in cacao ( Theobrama cacao L.) were fitted using leaves from cultivated plants under nursery conditions and from plants of commercial plantations, both located in the Amazon Investigations Center CIMAZ at Macagual, Caquetá, Colombia. A total of 2895 leaves were collected in such a way to cover a wide range of leaf sizes. Width, length, weight, and leaf area were measured for each leaf. The total number of leaves was randomly divided into training and validation sets. The training set was used for model fitting and selection, the other for measuring model prediction ability. Leaf area and leaf weight were modeled using different linear regression models based on length and width of leaf. Polynomial regressions involving both length and width of leaves provided very good models to estimate the expected area (R 2 = 0.98) and weight (R 2 = 0.91) of leaves. [ABSTRACT FROM AUTHOR]

Theobroma cacao gives higher yield when cultivated in full sun under irrigation system with fertilization, because is a species little conservative in relation the efficiency of water use. On the other hand, T. cacao is usually cultivated under shade conditions in ‘ Cabruca ’ and agroforestry systems but with low yield. It has been observed under field conditions that the genotypes of T. cacao with high concentration of anthocyanins in young leaves are more tolerant to high irradiance stress when grown in full sun. The accumulation of flavonoids or other UV-absorbing compounds in the leaf epidermis is one of the most important mechanisms to screening out UV-B radiation. The aim of this study was to evaluate the effects of different levels of light on three clonal cacao genotypes (‘Catongo’, SCA-6 and SJ-2), contrasting in relation to accumulation of anthocyanin levels in young leaves, by evaluations of photosynthesis, activity of guaiacol peroxidase (GPX), chloroplastid pigment contents and vacuolar (anthocyanins) flavonoids contents, anatomical characteristics and gene expression of the leaf. In summary, (i) the anthocyanins contents in leaf level did not provide protection against photoinhibition in T. cacao , (ii) the ‘Catongo’ and SJ-2 genotypes showed greater phenotypic plasticity to the morphology and the chloroplastidic pigment contents in the leaf, while the SCA-6 genotype allocated more in the flavonoids content and hsp70 gene expression; (iii) the relative expression of the genes psbA and psbO , did not vary between genotypes under irradiance stress. [ABSTRACT FROM AUTHOR]

• Fertilizer effects on cacao were studied on fruit, tree and plantation level. • Fertilizer application stimulated pod production in the late rain season in West Africa. • Fertilizer application increased pod size and bean content but not pod number. Fertilizer application in cacao production systems in West Africa yields highly variable results, ranging from no effect to doubling of the yield. Mechanisms underlying yield responses to increased nutrient availability are still largely unkown. In this study, we assessed how fertilizer application affects pod development and production of cacao trees in a full sun cocoa system in Côte d'Ivoire and a shaded cocoa system in Ghana. We monitored pod growth over time and the number of pods produced simultaneously on the trees in the minor and major harvest seasons. Furthermore, we measured nutrient concentrations in cherelles and beans and husks of developing pods in the major harvest season to estimate the total nutrients allocated to developing pods per tree. Lastly, we performed detailed yield measurements (number of pods, location in the tree (canopy or trunk), pod size and bean content) in 2020 for the plot in Côte d'Ivoire. Our results showed that, in the major harvest season, pods on fertilized trees grew wider (average: 15.4 cm) than pods on unfertilized trees (average: 11.9 cm). A higher pod growth rate resulted in a larger final pod size; larger pods took longer to mature. In the major harvest season, more cherelles on fertilized trees than on unfertilized trees reached maturity despite having an equal or lower nutrient content. Competition for assimilates rather than nutrients seems to induce cherelle wilt. In pods past wilting stage, fertilizer application slightly influenced nutrient dynamics of developing pods but not the final nutrient content in ripe pods. Lastly, increased nutrient availaibility did not change the absolute number of pods a tree produced annually. However, fertilizer application did increase the estimated annual dry bean yields from 2260 kg ha−1 to 2930 kg ha−1 by increasing the number of pods that developed during the major harvest season, when pods were heavier and the bean weight within the pods was relatively higher. [ABSTRACT FROM AUTHOR]

Growth and development of plants frequently are limited by multiple abiotic stresses that occur simultaneously in the environment. ‘Cabruca’ an agroforestry system is a main cropping system invariably adapted for cultivation of cacao in southern Bahia, Brazil. In this system of management, cacao is grown under the shade of native species of the Atlantic Forest. However, growing cacao under the shade of trees is still questionable due to higher incidence of pests and diseases and difficulty of evaporation of excess soil water in high rainfall periods that often causes flooding. The objective of the current study is to evaluate the performance of two clonal genotypes of cacao, contrasting for tolerance to soil flooding (TSA 792 – tolerant and TSH 774 – intolerant), subjected to four levels of light intensity and two water regimes, control and flooded, in order to elucidate the mechanisms of tolerance to these stresses under ‘Cabruca’ environment. All the plants survived the period of flooding, however, with flooding stress visual symptoms like leaf chlorosis, lenticels hypertrophied on the stem base, and decomposition of roots were observed. Obtained results demonstrated morpho-physiological and molecular changes in response to low light intensity and low light intensity × soil flooding interaction. Significant effects (p < 0.05) of isolated factors, double interaction and inter- and intra-genotypic differences (p < 0.05) were observed for leaf gas exchange, chlorophyll fluorescence, and growth parameters. Differences among light intensities, water regime, plant organ (p < 0.001), and for the interactions low light intensity × water regime and water regime × plant organ (p < 0.01) were observed with respect to total soluble sugar content. Isolated factors and double and triple interactions (p < 0.01) had significant effects on the starch accumulation. Triple interaction was also observed in the expression of genes coding for ADH, LDH and PDC enzymes and for aquaporin PIP1;2. Low light intensity interacts with soil flooding, limiting the damages caused by flooding in cacao plants under lowest light intensity. Flooding was the dominant factor for the most physiological responses observed during the interaction between light intensity and soil flooding whose physiological adjustments were different amoung the clonal cocoa genotypes assessed. [ABSTRACT FROM AUTHOR]

• PH 16 genotype exhibited better photosynthesis, accumulation of sugars, and lignin in full sun. • PH 16 and "Ipiranga" 01 genotypes showed higher dimensions of the fruits and the chemical quality of its almonds in full. • In winter, the C assimilation from "Ipiranga" 01 genotype was higher in 20% of PPFD. Traditionally cultivated in the understory of tropical forests, the cultivation of Theobroma cacao in full sun is expanding. Under this irradiance, photosynthesis of some genotypes is stimulated in the juvenile stage. In adulthood, little is known about the effects of full sun on this physiological process, as well as on the antioxidant metabolism, fruit growth, and the chemical properties of its almonds, especially under the influence of precipitation and temperature variations. In this study, we analyzed gas exchange, chloroplast pigments (chlorophylls and carotenoids), and antioxidant compounds (polyphenols, flavonoids, anthocyanins, lignin, and sugars) in adult plants of the PH 16 and "Ipiranga" 01 genotypes, grown in a gradient of artificial solar irradiance (20–100% of photosynthetic photon flux density - PPFD). Analyses were performed in winter and summer. The dimensions of the fruits and almonds and the chemical quality of the almonds were also provided. Plants of the PH 16 genotype exhibited better photosynthetic performance, accumulation of sugars, and lignin when grown in full sun, during both seasons of the year. This response was repeated in the "Ipiranga" 01 genotypes only in the summer. In winter, the C assimilation from this genotype was higher in the severe shade (20% of PPFD). Higher contents of chloroplast pigments, flavonoids, and anthocyanins occurred in both genotypes in 20 and 50% PPFD. On the other hand, full sun increased the polyphenols, lignin, and sugars levels. The cultivation of genotypes PH 16 and "Ipiranga" 01 of T. cacao in full sun provided larger dimensions of fruits/almonds (fruit size, number of almonds per fruit, and dry mass of almonds) and higher chemical quality (pH, titratable acidity, and total fat) of its almonds. The results allowed us to conclude that the cultivation of genotypes PH 16 and "Ipiranga" 01 of T. cacao in full sun increased the physiological quality of the plants, the dimensions of the fruits/almonds, and the chemical properties of its almonds. [ABSTRACT FROM AUTHOR]

In cocoa cultivation pruning is considered an essential yield-enhancing practice but its effects on cocoa tree growth and yield, and how these are mediated by tree size and competition are poorly understood. Here, we evaluate the impact of experimental pruning on: light interception, leaf flushing and the number of flowers and of developing, wilted and harvested pods. The pruning treatment removed an average 26.4% of cocoa tree aboveground biomass and was aimed to create an open cup-shaped crown. Stem basal area and sum of neighbor tree basal area were used as proxies for tree size and tree competition, respectively. All response variables were analysed at tree level as a function of pruning, tree size and tree competition using generalized linear mixed effect models. After one year, pruned trees recovered initial losses in whole-canopy light interception but maintained a more uniform distribution of light in the canopy. Pruning directly increased flushing activity, while the effect on the other variables was mediated by the interaction with tree size and competition. Pruning increased the positive effect of tree size and competition on flower number and similar effects were found for small pod number. The latter effect was counterbalanced by an increase of pod wilting in pruned trees under high competition, resulting in similar numbers of large and harvested pods on the stem in pruned and unpruned trees. For pods in the canopy, pruning did enhance the positive effect of tree size and strongly reduced the negative effect of competition on pod number. As canopy pods made up 60% of the total, similar pruning effects were found for the total number of harvested pods. The predicted net effect of pruning on the number of harvested pods varied greatly with tree size and competition, ranging from -58% for small trees under low competition, to +150% for large trees under high competition. This large variability stresses the importance of individual-level analysis to quantify pruning effects and calls for more attention to individual tree characteristics in training and practice of cocoa pruning. The pruning-induced reduction of negative competition effects suggests that pruning can contribute to realizing high-density cocoa stands. [ABSTRACT FROM AUTHOR]

• A total of seven LchiPYL genes were comprehensively identified and characterized in the Liriodendron chinense genome. • LchiPYL genes were highly conserved in plant species. • The expression patterns of seven LchiPYL genes in buds responding to ABA, photoperiod, and chilling stress were established. Abscisic acid (ABA) is a signaling phytohormone in plants to improve stress adaption under harsh environments. ABA is sensed by the pyrabactin resistance1/PYR1-like/regulatory components of the ABA receptor (PYR1/PYL/RCAR) (named PYLs) and is the core regulator of ABA stress signaling. ABA receptor PYL gene family have been well studied in rubber tree, apple, Theobroma cacao, Ricinus communis , and Vitis vinifera. We first revealed the genome-wide comprehensive analysis to classify the PYL genes in the L. chinense. This study highlighted the seven LchiPYL genes in the L. chinense genome. The detailed investigations about gene structure variations, chromosomal distributions, phylogenetic tree, 3D structure, motif analysis, cis-regulatory elements, subcellular location, and expression profiles in buds and stress responses were carried out in this article. Phylogenetic tree analysis exploited that the seven LchiPYL genes were divided into four groups (Group I–IV) from L. chinense, and three were highly linked with other species. By analyzing the cis-elements in the promoters, we identified five hormones-, six stress-, three growth and biological process, and two metabolic-related responsive elements. The expression analysis showed that all seven genes were up-and down-regulated against response to ABA, photoperiod, chilling, and chilling + photoperiod treatments. Our findings opened up new future research directions and provided insight into the PYL family genes in Liriodendron chinense. [ABSTRACT FROM AUTHOR]

• Scion-rootstock interaction interferes in tolerance to Cd toxicity in T. cacao. • Cd accumulation in rootstock mitigates to Cd toxicity in T. cacao shoot. • Intergenotypic differences between scion-rootstock of T. cacao interfere in Cd uptake and transport. Cadmium (Cd) is a highly toxic metallic element for plants, animals and humans. The presence of toxic metals in food has been a concern of the Food and Agriculture Organization of the United Nations. Several studies have demonstrated the presence of Cd in T. cacao beans and its by-products. The contents are found to be above the limits established by international authorities responsible for food safety. This study aimed to evaluate the toxicity of Cd in different genotypes of T. cacao , in scion-rootstock combinations (CCN 51/BN 34, CCN 51/PS 13.19, CCN 51/PH 16, CCN 51/CCN 51, BN 34/BN 34, PS 13.19/PS 13.19 and PH 16/PH 16). The combinations were grown in soil with 0, 75 and 150 mg Cd kg−1 soil. The measurements for evaluation were leaf gas exchange, activity of enzymes involved in antioxidant metabolism and lipid peroxidation. Cd promoted physiological and biochemical changes, in the scion-rootstock interaction, in juvenile T. cacao plants. The combinations CCN 51/BN 34 and CCN 51/PH 16 demonstrated tolerance to the toxicity of Cd in the soil, mainly evidenced by the higher accumulation of Cd in the root system, higher carbon assimilation, higher activity of superoxide dismutase, ascorbate peroxidase and catalase, lower lipid peroxidation and higher water use efficiency in the presence of Cd. The combination CCN 51/BN 34 shows promising potential to be grown in soils contaminated by Cd. [ABSTRACT FROM AUTHOR]

• oxdc gene from flammulina velutipes was used to generate transgenic tomato plants. • Transgenic T 1 lines showed a significant delay in symptom development. • Transgenic T 1 lines showed a higher survival percentage to witches' broom disease. • The P16 line showed a decreased production of H 2 O 2 in the presence of oxalic acid. • Witches' broom disease progression was reduced by the presence of the oxdc gene. Witches' broom disease which affects cacao tree (Theobroma cacao L.) is caused by the hemibiotrophic fungus Moniliophthora perniciosa. Studies of the cacao- M. perniciosa interaction showed that the pathogenicity of M. perniciosa is associated to the presence of oxalic acid (OA). In some organisms, OA can be degraded into formate and CO 2 by the oxalate decarboxylase (OXDC) enzyme. Here, we used the oxdc gene from Flammulina velutipes to generate transgenic tomato plants as a potential strategy to control M. perniciosa infection. Three transgenic T 1 lines expressing the oxdc gene were obtained and two of them (P4 and P16) presented a significant delay in symptom development and higher survival percentage when inoculated with M. perniciosa in comparison to the non-transformed wild-type (WT) plants. Moreover, the P16 line test showed a decreased production of H 2 O 2 in the presence of OA in comparison to the WT, as evidenced by the 3,3′-diaminobenzidine test. These results indicate that the P16 transgenic line is able to break down OA leading to normal plant development with few symptoms even when infected by M. perniciosa. Phenotypic and histological analysis showed differences between WT and transgenic plants. The amount of fungus hyphae was lower with thinner thickness in the transgenic plants. This study evidences of the reduction of witches' broom disease progression by the presence of the oxdc gene leading to the plant survival. [ABSTRACT FROM AUTHOR]

• Factors that influence Cd absorption by cocoa were soil pH, soil Cd availability and genotype. • The main strategy used by cocoa to reduce Cd toxicity is uptake and transfer of Cd and molecular changes. • CCN51 genotype had lower Cd concentrations than other genotypes. Cadmium (Cd) is a non-essential trace metal, highly toxic to plants, animals and humans. Its mobility in the soil is high and it is transferred with relative ease to crops. European Food Safety Agency (EFSA) has identified the consumption of chocolate as a source of Cd contamination, and established maximum Cd limits allowed in cacao-based products. Therefore, research related to tolerance and reduction of Cd toxicity in a cacao becomes important. The main objective of the present study was to systematize the main factors that interfere in the uptake of soil Cd by the cacao tree and its strategies for tolerance to toxicity. A systematic review of the literature was conducted using six databases for academic research (Google Academic, PubMed, Springer, CAPES Periodical, Scielo and Science Direct). To avoid publication bias, a previously established protocol and inclusion and exclusion criteria were used. The main factors related to the uptake of soil Cd by the cacao tree were soil pH, soil Cd availability, genotype, the geographical location, agronomic factors such as phosphate fertilizersand Cd interaction with other minerals/metal nutrients such as Zn and Mn present in the soil. To reduce the toxicity of this metal, cocoa promotes some tolerance strategies such as uptake and transfer of Cd from the root to the shoot, molecular and biochemical changes, Cd partition between plant organs and Cd sequestration at the cellular level. So, this systematic review contributed to the acquisition of knowledge for the genetic improvement of cacao tree, concerning toxicity tolerance strategies and reduction of soil Cd uptake. [ABSTRACT FROM AUTHOR]

Abstract: Understanding the relationship between vegetative vigor and productivity in cocoa is critical to maximizing yield per unit area in cocoa plantations. Three trials established from either progenies of self mating of 24 clones of Upper Amazon origin, or from progenies of mating among clones recommended as parents for production (Seed Garden clones) or from progenies of inter- and intra-group mating of selected clones were analyzed for their vigor and yield relationships over a period of 10 years. The rate of increase in tree trunk cross-sectional area (TCSA) prior to bearing was an effective parameter in identifying families with large cumulative yields over the first five or six production years. Families with slow increase in juvenile TCSA were particularly of low bean yields. Though girth of adult trees was generally correlated with cumulative yields, a consistent relationship between tree girth at the end of the 10th year and yield efficiency was not observed. Yield efficiency was significantly correlated with cumulative yield, and showed predominantly additive gene action. The combined selection for rapid increase in juvenile tree TCSA and precocity have the potential of identifying high yielding families early in a cocoa breeding program. [Copyright &y& Elsevier]

• Compatibility depends on the pollen genetic origin and is less successful within many Trinitario clones. • Agronomic traits can be improved when plants are in desirable nutritional status by varying pollen donor genetic origin. • The pH of beans after postharvest practices and the average weight of one dry bean are good indicators for chocolate makers. • Cut-test daily colors are a rapid tool to classify dry cocoa beans into several grades. Incompatibility within and between cocoa trees or cocoa clones is incontestably one of those factors which reduce cocoa yield in fields. Indeed, the traceability of raw materials is one of the major challenges that agro-industries face today. Improvement of cocoa and cocoa products' quality passes through the identification of cocoa genetic and geographic origin as well as the farm where cocoa is produced and harvested. Hand-pollination was used to assess compatibility between clones, to select interested agronomic traits (pod length, pod cortex thickness, average beans number, average beans weight, average weight of fresh or dry beans) and to improve specific cocoa beans quality through physicochemical parameters after post-harvest practices. Three different parents were used as female-clones: ICS40 (higher Trinitario), SNK16 (Trinitario), SCA12 (Lower Amazon Forastero) and four clones added to the female ones as pollen donors: SNK16, SNK13 (Trinitario), UPA134 (Upper Amazon Forastero), T79/467 (Amelado, Forastero), T60/877 (Amelado, Forastero), ICS40 and SCA12. Crosses within Trinitario clones showed a low level of compatibility (0–18%) whereas the general combination ability between Trinitario×Forastero (59–81%) and within Forastero (84–88%) and between Forastero×Trinitaro (78–88%) was very promising. SCA12 showed a high level of compatibility efficiency compared to the two Trinitario female-clones studied. The pollen grains from SCA12 increased the pod length and average weight of fresh beans in ICS40 female-clone meanwhile those of T60/877 also increased the pod cortex thickness and average weight of fresh/dry beans in SNK16 female-clone. The genetic description of each pollen clone donor played a key role in the resulting hybrids. The pH values of fermented dried beans, ranged from 5.31 to 6.26 and was female-clone dependent. A strong negative correlation was observed between the average beans weight (fresh or dry) and pH. These results highlighted that the genetic origin of pollen grains could increase compatibility between clones, agronomic traits and consequently the physicochemical parameters of beans. [ABSTRACT FROM AUTHOR]

• There is a high general combinatorial ability in genetic compatibility of cacao clones among groups from different geographical origins. • For the establishment of a cacao plantation, a combination of self-compatible and inter-compatible cacao clones should be selected. • All cacao groups achieved high performance with either a male or a female receptor, or in combination, except for the CAUCASIA group. • By using an optimal crossing clone combination, over 80% of fruit set could be achieved. Sexual self-incompatibility is a very salient trait of woody plants, including cacao (Theobroma cacao L.). In this species, most commercial clones are self-incompatible and, therefore, productivity depends on pollen flow for fruit formation due to the combinatorial ability of each clone to accept or reject pollen tubes in the embryo sac. To determine the combinatorial ability of commercial cacao clones, artificial (manual) pollinations were performed between cacao clones of the same and between groups for three years. In total, 46 cacao clones of five geographical groups were evaluated: 'FHIA' from Honduras, 'ICS' from Trinidad and Tobago, 'UF' from Costa Rica, 'CAUCASIA' from Colombia, and 'EET' from Ecuador. The results showed that, except for 'CAUCASIA', there is a high level of inter-compatibility between groups. Cacao clones exceed the established threshold of 30% in Fruit Set Success when used as a female or a male donor. As expected, low self-compatibility rates were found among the clones studied. We propose the use of sexual inter-compatibility information for the design of planting arrangements to maximize cacao yields. [ABSTRACT FROM AUTHOR]

• Photosynthetic plasticity between sun and shade leaves of Theobroma cacao (WAA) was investigated. • Increased capacity for photosynthesis in sun leaves however they were subject to photoinhibition. • Sun and shade leaves demonstrated typical pigment plasticity. • No observed plasticity in superoxide dismutase activity between the sun and shade leaves. • Increased activity of ascorbate peroxidase and catalase was observed in sun leaves. Theobroma cacao is a tropical understory tree that is traditionally grown in an agroforestry system under a shade canopy; but is increasingly being grown in an orchard system with limited shade or no shade. This study investigated the light response of sun and shade leaves from mature trees of one of the most cultivated cacao accession (West African Amelonado), grown under full sun conditions. Chlorophyll fluorescence was used to measure F v /F m , and to generate light response curves for photosynthetic and non-photosynthetic quenching parameters. The light response curves indicated an increased capacity for photosynthesis in the sun leaves however the F v /F m and NPQ data showed that the sun leaves were subject to photoinhibition. Biochemical assays were used to compare sun and shade leaves for photosynthetic pigment content and a range of parameters related to reactive oxygen species scavenging and cellular damage. The sun and shade leaves demonstrated typical pigment plasticity however the chlorophyll carotenoid ratio was low for both types of leaves. There was no observed plasticity in superoxide dismutase activity between the sun and shade leaves however the plant was able to respond to the increased photosyntheically active radiation by increasing the activity of ascorbate peroxidase and to a lesser extent catalase. Increased electrolyte leakage in the sun leaves however suggests that the ability to mitigate reactive oxygen species was limited. The results point to limitations in the ability of currently cultivated cacao to acclimate to full sun conditions. [ABSTRACT FROM AUTHOR]

• The cuprous oxide fungicide induces imbalance in cellular metabolism in young cocoa leaves. • Copper toxicity promotes changes in carbon assimilation and antioxidant metabolism. • There is synergism in the cell detoxification pathway between enzymatic and non-enzymatic antioxidants in the removal of ROS. Copper (Cu), besides being an essential micronutrient for plants, is a component of fungicides used in cacao farming. The objective of this study was to evaluate Cu toxicity in leaves of young plants of cocoa genotype CCN 51, applied via the leaf as cuprous oxide fungicide at different concentrations (0, 1.5, 3, 4.5 and 6 g Cu L−1) by means of physiological, biochemical, molecular and nutritional changes at leaf level. Cu concentrations (4.5 and 6 g Cu L−1) applied via leaf severely affected leaf gas exchange, promoted changes in the activity of superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPX) and ascorbate peroxidase (APX) enzymes, free proline concentration, lipid peroxidation and expression of the genes psbA , psbO , Mt2b , sod cyt , sod chl and per-1 , as well as changes in concentration of mineral macro and micronutrients in leaf. It was concluded, therefore, that the application of different concentrations of Cu via cuprous oxide fungicide to leaf induced an imbalance in the leaf metabolism of the young plants of CCN 51, through modifications in leaf gas exchange, in the activity of the enzymatic and non-enzymatic antioxidative metabolism, in the expression of genes related to oxidative stress, photosynthesis and mechanisms of cellular detoxification. In addition, a dose-dependent type response pattern was verified, indicating that there was a synergism in the cellular detoxification pathways in eliminating excess reactive oxygen species (ROS). [ABSTRACT FROM AUTHOR]